


Chuck versus That Good Night

by Peril_in_Peace



Category: Chuck (TV)
Genre: Alternate Ending - Chuck vs. Phase Three, Brain Damage, Computer Jargon, F/M, Season/Series 04
Language: English
Status: Completed
Published: 2018-02-04
Updated: 2018-02-04
Packaged: 2019-03-13 09:16:12
Rating: General Audiences
Warnings: No Archive Warnings Apply
Chapters: 1
Words: 2,610
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/13567476
Author URL: https://archiveofourown.org/users/Peril_in_Peace/pseuds/Peril_in_Peace
Summary: After the massive damage already done by the Belgian's machine, simply disconnecting the wires and crying and kissing him like Sleeping Beauty... did Sarah really think that would be enough to magically save him?Alternate ending to season 4's Chuck vs. Phase Three.





	Chuck versus That Good Night

**Author's Note:**

> Written several years ago, and found whilst cleaning out the ol' Google Drive. Originally intended to be longer... but I've never posted to Chuck fandom... figured it was worth putting out there as is. Might continue if there's interest... I know the show has been (unfortunately) gone for a very long time. But there's always the DVD's... 
> 
> Man, I really miss them... 
> 
> Anyway... Thanks for reading. If you're out there. :)

“You’re too late. He’s almost completely gone.” 

She’d cried. She’d begged him to wake up. Told him how much she loved him. What did she expect? That somehow his destroyed brain would hear her and put itself back together again?

Whatever the Belgian had done, he’d done it well. Thoroughly. He really was completely gone.

Sarah glanced over at Chuck. At his shell. His eyes were open, he sat up straight, head turned to stare blankly out the Gulfstream’s window. Morgan sat across from him, fighting to stay awake. As if closing his eyes would cause him to miss a glimmer of Chuck rising to the surface. She knew the feeling, but made herself turn away.

“Beckman’s prepping a team at Quantico. We’ll get him back there and the company shrinks will figure it out.” Casey was trying to make her feel better. It was kind--but not particularly effective.

“Yeah,” Sarah mumbled. “They’ll figure it out.” But her heart beat in her throat.  _ No they won’t. _

She had been on the warpath. So focused on finding him and bringing him home, but now… she sighed and looked across the aisle again. He hadn’t moved, still stared out the window, nobody home. The feeling of dread and defeat was enough to choke the breath out of her. With every fiber of her being she knew the war was simply… over. Chuck was gone.

* * *

 

“Well, General, I wish I had better news but, as I told Chuck some time ago, the Intersect and how it works with the human brain could barely be considered science. We’re doing our best to navigate through murky and uncharted waters,” Dr. Dreyfus said, folding his hands over his lap.

Sarah bit the inside of her cheek as Beckman closed Dreyfus’ report on her desk. Casey crossed his arms and stared out the window of the Generals’ office.

“Does Chuck remember… anything?” Beckman asked, gently pulling her reading glasses from her nose and setting them down beside the report. Dreyfus shook his head.

“Of his own life? Nothing, it seems. Of the state secrets stuffed into his brain? The Intersect is totally intact. According to this Belgian fellow, that was the point. We have tested the Intersect and found that the Belgian’s procedure did work--it targeted Chuck’s own memories leaving only the program behind.”

“Well, that’s something, at least,” Beckman said. Sarah glared at her, but held her tongue.

“All due respect, General, screw the Intersect,” Casey said what Sarah was thinking.

“Colonel?” Beckman inquired. Casey turned away from the window.

“Chuck Bartowski has served his country well. He’s done everything you’ve asked of him and then some. I never thought I’d say it, but the wrong asset made it through this.”

“This may come as a surprise to you, Colonel Casey, but I don’t disagree with you that Chuck is an asset with or without the Intersect. I mean to say that with the Intersect intact, we may have some… options.”

Sarah furrowed her brow at the General. “I don’t understand.”

Beckman nodded to Dreyfus, who unfolded his hands and sat up a little straighter. “Agent Walker,” he began. “I understand that Chuck has not always been forthcoming with you about his challenges with the Intersect. I hope you know that his first concern has always been for you. When his mind started to deteriorate several months ago, he didn’t want to worry you.”

Sarah nodded.

“You should know that he’s been seeing me fairly regularly since then. With the exception of his... sabbatical... from the CIA, of course.”

“He didn’t tell me.”

“I know,” Dreyfus continued. “Like I said, he--”

“Didn’t want to worry me.”

He nodded. “He continued seeing me not so much for therapy, but to gain more insight into how the Intersect works. To develop his control over it and, ultimately, he hoped to develop ways to continue using the Intersect safely and protect himself from any further ‘crashes,’ as he put it.”

Casey shrugged. “...Such a geek,” he mumbled.  

Sarah couldn’t help but smile.

“Frankly, we’ve made some progress. Together, we’ve tried to develop some mental exercises for him to try and streamline his access to the Intersect.” He paused, considering how to continue. “...As you know, he relies on a sensory stimulus to trigger a flash and unconsciously access the pertinent information from the computer. Chuck has been working on trying to access the Intersect  _ consciously _ \--on command,” Dreyfus explained.

“I’m sorry, Doctor, I still don’t understand how this helps us. Chuck’s brain was destroyed--who cares if he can access the Intersect?” Sarah said, crossing her arms and leaning back in her chair.

Dreyfus shook his head. “That’s just it, Agent Walker. I’m not convinced that his brain  _ is _ destroyed. I’ve studied the specifications of the equipment that was recovered from where Chuck was being held…”

“Not destroyed?” Casey interjected. “What does that mean?”

“To build on the computer analogy--I believe that his hard drive is intact, but it is… no longer connected to the motherboard. The machine the Belgian used seems to have fried the contacts, but left the data intact. Which makes perfect sense, really, if the goal was to access the Intersect--causing destruction within the brain would inevitably result in damage to the very data he was trying to extract.”

Sarah pursed her lips. “So what you’re saying is… Chuck’s still in there…?”

“It’s difficult to be certain, but based on our preliminary CT scans and MRIs… that is my conclusion.”

“So how do we get him ‘out?’” Casey asked.

Dreyfus took a deep breath. “When Chuck...  _ flashes _ , the Intersect functions by building a new neural connection between the computer and Chuck’s brain, transferring the data into his short term memory. At that point, he essentially learns the information like he would anything else… any other information he might consume. When we sleep, information is moved from short term to long term storage, in a different part of the brain. This is why his first symptoms of the Intersect’s failure surfaced in dreams.

“I believe that we can  _ use _ that functionality of the Intersect. The Belgian’s device basically cut existing neural connections in Chuck’s brain, cutting  _ him _ off and making his memories inaccessible.”

“I thought that brain damage like that was permanent. If those connections have been damaged, they can’t be repaired,” said Sarah. Dreyfus nodded.

“For the most part, that’s very true. However, the human brain is incredibly resilient. While the damaged connections can’t be  _ repaired _ , we  _ can _ stimulate new ones being  _ created _ . I believe we can use the Intersect to accomplish this, much in the way a stroke victim can relearn lost skills through rehabilitation. It’s a relatively new principle, but neuroplasticity has been well-proven and the science is making rapid progress.”

“Do you know how to do that?” Sarah asked, looking the doctor directly in the eye. “I mean, we’re not talking about relearning how to hold a fork--we’re talking about relearning a lifetime of memories and skills.”

Dreyfus took a deep breath and shook his head. “That is where we run into some problems. The Intersect is complex. The only person who truly understood how it works…” He swallowed and looked at his folded hands in his lap. “Well... I understand Orion is no longer with us. That being the case, I have no doubt that solving this problem will take a good deal of  _ time _ … but with that time and further study, I believe it can be done.”

“And until then… Bartowski’s what… a mindless lab rat?” asked Casey.

Beckman interjected. “I see no other alternative, Colonel. We will put all the resources we can into bringing Chuck back.”

“General…” Sarah started tentatively. “What if we  _ did _ have an expert on the Intersect?”

“I assure you, all of our experts will already be on the case,” replied Beckman cautiously.

“Not all of them, General. What about Chuck’s sister?” Sarah clarified. Beckman’s took a deep breath.

“Agent Walker, I’ll be honest with you--given her background in neurology and her recent progress on the work Orion left her--it did cross my mind to authorize you to bring Ellie in on this. But…” Beckman continued, “Do you really believe that’s what Chuck would want? It has always been his highest priority to isolate his family from his work with the agency.”

“General, while this may not be what Chuck would want… I’m pretty sure it’s what Ellie would want. Let me talk to her,” Sarah said. Beckman nodded. 

“Very well. Talk to Dr. Woodcomb. See what she knows about the Intersect. We’ll send you all back to Burbank where you can work out of Castle. Please continue to consult with Dr. Dreyfus, but… we’ll try this your way first.” 

* * *

 

Chuck opened his eyes, then blinked, lifting his arm to block out the light of the room. He sat up. The room was all white. There was a gray computer in the middle that looked like an old Apple IIGS. A blue object was in the base beneath it. The glow reminded him of the tower backlight on a gaming rig he… sort-of remembered building once. 

The room looked familiar. But he couldn’t quite place it. 

Chuck walked up to the computer. The green text on the screen read “Press ENTER to begin.” He squinted at the screen and looked around. He caught himself and wondered who he was looking for. 

“Begin what?” he mumbled to himself and took a slow walk around the computer’s pedestal. He had a sinking feeling in the pit of his stomach. He was forgetting something. Lots of somethings. He  _ felt _ like he should know what this was and what was happening, but he just couldn’t find the information he knew he needed. His head hurt.  

He opened up his inspection to the outer walls of the room. The floor, walls and ceiling all looked exactly the same. He couldn’t find a door. So Chuck directed his attention to the floor, looking for an access panel to the wiring that he instinctively thought should be underneath him, but there were no edges he could slip his fingers under to lift. 

He sighed and returned to the computer. Chuck stuck his hand out and hovered his index finger over the enter key. His gut fluttered oddly. This felt so familiar. 

Chuck pressed enter. The screen went blank. His heart sank--he was sure something… important… should have happened. He pressed enter again. Nothing happened. He followed his next instinct and grabbed the computer, turning it around to access the input cables to make sure the keyboard was plugged in. It was. He pressed enter again. Then the spacebar. Nothing happened. 

He shook his head and ran his hand through his hair in frustration. Then he turned around to check the outer walls for a door again. Maybe he’d missed something before. 

“Hello, Chuck.”

Chuck stopped short, narrowing his eyes at the man who had seemingly appeared out of nowhere. He hadn’t been there before… had he?

“Dad?” he asked.

Stephen shook his head. He looked… younger. Chuck had an image in his mind from somewhere… that his dad should look older, frazzled. But here… he looked almost dapper. He wore a clean, smartly pressed but casual gray suit. His hair was cut and neat.

Chuck pursed his lips. “You’re… not my dad.” It was halfway between a question and a statement.

“No.”

“Then who-- _ what _ are you?”

“I am the Graphical User Interface for the Intersect computer. I am designated as the Objective Response Internal Operations Node for this system. You may refer to me as ORION.”

Chuck’s head hurt. It throbbed. He sat down hard, pulling his legs into his chest and dropping his forehead on his knees.

“We’ve never met like this before,” ORION said. “But we’ve been working very closely together for quite some time.”

“I should know what the Intersect is,” Chuck stated, more to himself than the GUI.

“You may find it difficult to remember some things right now. We’ll work together to restore functionality, but it will take some time.”

Chuck lifted his head and looked carefully at the not-Dad image. “What do you mean, “restore functionality? What happened? Where am I?”

“This is the Clean Room. We are in Quarantine. You are a compilation of the data I was able to back up onto this partitioned drive before catastrophic hardware failure,” ORION answered matter-of-factly.

“I don’t understand.”

“What is the last thing you remember?”

“I…” Chuck thought hard for a moment. Images flashed through his mind… people he didn’t quite recognize, places that felt familiar but that he didn’t really know. Everything was mixed up. “I don’t know. I can’t… focus… I can’t focus on anything specific. I don’t know what any of it means.”

The GUI nodded. “Please wait. Defragmenting drive.”

Chuck’s headache went away. The bright white light of the room seemed to dim to a more comfortable level. “What did you do?” he asked.

“I must apologize for the earlier… disorganization… you experienced. There was very little time to run the Quarantine protocol, and I’m afraid the executable only reached 67.8% completion. You will continue to experience missing data, however I have identified holes in your logic runtime and input placeholder code to reduce the negative side effects.”

“You’re talking like I’m in a computer or something.”

ORION blinked. “You are.”

“What?” Chuck shook his head. “Please explain.”  

“This is the Clean Room. We are in Quarantine. You are a compilation of the data I was able to back up onto this partitioned drive before catastrophic hardware failure.”

“You said that already.”

“That is the correct response to your query. For more information, please specify additional parameters.”

Chuck shrugged. His head was feeling much more clear and the questions now started to flow freely through his mind. “Clarify the term quarantine. Identify location and purpose.”

“Quarantine is a partitioned drive of the Intersect computer primarily housing relocated files determined to be harmful to the system. The Clean Room is a secondary function of the Quarantine protocol designed to isolate Master Files in the event of system-wide corruption and to allow reboot into Safe Mode.”

“What system?”

“The system to which I refer is comprised of two interdependent computers: the Intersect computer and the Host computer. The Intersect computer functions via virtualization utilizing the Host computer’s hardware, memory and processing resources.”

“Identify the Host computer.”

“The Host computer for this system is identified as Charles Bartowski.”

“Identify Intersect computer.”  

The room went dark. Chuck stood up quickly, disoriented. He looked for a point of reference in the blackness.

The green cursor blinked on the IIGS. Then the walls, floor and ceiling lit up with flashing images.

And for the first time since waking up, Chuck understood that something was outside this room that he  _ needed _ to get back to.

* * *

 

Sarah took a deep breath before knocking on the door. She’d run the conversation she was about to have a million times in her head. Sarah had supported Chuck’s decision to keep Ellie in the dark about returning to the CIA at the time… but now, she wished the news had come from him. Ellie was going to hate her.

But it didn’t matter. As long as Chuck was okay, it didn’t matter. Ellie could hate her until the day she died, and it wouldn’t matter. It was a small price to pay. If there was any chance she could help Chuck, any chance to bring him back… 

It may not be fighting her way through Thailand. But any battle was worth fighting for this.    
  



End file.
